The point is not that New Atheists are necessarily homophobic. The point, rather, is that New Atheism is a form of bigotry, and, therefore, it necessarily resembles other forms of bigotry.
New Atheism is a form of bigotry because it is based on irrational fear and hostility directed at people based solely on their religious beliefs. And like other forms of bigotry, New Atheism doesn't stop at disparaging religious people, but actively seeks to harass and discriminate against them because of their religiosity, and even has the stated goal of eventually ridding the world of religiously minded people altogether.
1. Special Rights/Religious Privilege
Homophobia: The right-wing website Conservapedia in their entry on "The Homosexual Agenda" cites Joseph P. Gudel to the effect that "the homosexual movement":
has been militantly demanding not just the homosexuals' right to do whatever they wish to do behind closed doors, but, more importantly, that society fully accept their lifestyle as both healthy and normal, even demanding special rights and legislation as an "oppressed minority."New Atheism: Austin Cline, a Fullbright scholar and prominent Atheist blogger wrote a piece for About.com titled "Equal Rights vs. Special Rights":
If a person has a sincere religious belief, they can apply for — and are usually granted — exemptions from generally applicable and neutral laws. Employers, too, are required to accommodate people’s religious beliefs even if this means exempting them from generally applicable, neutral rules in the workplace. Religious believers enjoy a broad array of special rights and privileges unavailable to others who may want exemptions for non-religious reasons.2. "They don't keep it to themselves"
Homophobia: Scientific studies have shown that even "gay friendly" heterosexuals are often "disgusted" by public displays of same-sex affection. It is hardly news that homophobes often protest that they don't have anything against gay people so long as they keep it to themselves and don't flaunt it. A more specific example: Speaking on the right-wing Christian radio program "Washington Watch Weekly", U.S. Rep. Steve King (R. IA) stated that "If you don't project it, if you don't advertise it, how would anyone know to discriminate against you?"
New Atheism: "We aren't interested in what public officials do in their free time. They can have whatever legal hobby they want, they can favor whatever private rituals they want, they can associate with any non-dangerous group on their weekends that they want, whether it's going to church or gathering to watch football. So what's different about Collins? He doesn't keep it to himself. He is openly and avidly evangelical." P.Z. Myers in his aptly titled blog post "Is it really that hard to understand?"
3. Religion as mental illness
Homophobia: Dr. James Dobson, founder of Focus on the Family and a licensed clinical psychologist, has stated that he "and many others in the mental health field see homosexuality as a developmental condition stemming from a combination of factors — including, but not limited to, dysfunctional family relationships," and that this "developmental condition . . . can be overcome."
New Atheism: Sam Harris: "It is merely an accident of history that it is considered normal in our society to believe that the Creator of the universe can hear your thoughts while it is demonstrative of mental illness to believe that he is communicating with you by having the rain tap in Morse code on your bedroom window." Also: "It is difficult to imagine a set of beliefs more suggestive of mental illness than those that lie at the heart of many of our religious traditions."
4. Religion as a kind of contagion
Homophobia: A team of University of Arkansas psychologists studied the underlying emotions and attitudes behind homophobia. They used the Padua Inventory (psychological test for assessing "contamination obsessions") and other psychological tests, including the Index of Attitudes toward Homosexuals. They concluded that homophobia is based on "feelings of disgust" and "a perception of contagion".
New Atheism: Jerry Coyne wrote in a blog post titled "Francis Collins pollutes science with religion": "I am more certain than ever that Collins really does pollute his science with his faith. By speaking with the authority of a scientist, by discussing science at length, and above all by describing in the same talk the evidence for evolution and the 'evidence' for God, acting as if they are of similar epistemic significance, he is confusing his audiences about the nature of evidence and the nature of science . . . It’s a disquieting performance, even more distressing because Collins is an affable and genial speaker, conveying his snake oil is with a dose of sugar . . . He is polluting science with faith — and hurting public understanding of science." Also this from Sam Harris: "There is no question but that nominally religious scientists like Francis Collins and Kenneth R. Miller are doing lasting harm to our discourse by the accommodations they have made to religious irrationality."
5. Religion as a major cause of societal ills
Homophobia: It is well known that some Christians don't even stop at blaming social problems on the sin of homosexuality. Natural disasters and even terrorism can be caused by God's Wrath Over Homosexuality, according to such varied experts in theodicy as John Hagee, and Jerry Falwell.
New Atheism: Sam Harris sounds a lot like Rev. Hagee in his unhinged essay "The Problem With Religious Moderates": "Religious moderates are themselves the bearers of a terrible dogma: they imagine that the path to peace will be paved once each of us has learned to respect the unjustified beliefs of others. I hope to show that the very ideal of religious tolerance -- born of the notion that every human being should be free to believe whatever he wants about God -- is one of the principal forces driving us toward the abyss." Similarly, Richard Dawkins wrote in his The God Delusion that "even mild and moderate religion helps to provide the climate of faith in which extremism naturally flourishes." [p. 303]
6. "Dread of being in close quarters"
Homophobia: Psychologist George Weinberg is credited with first coining the term "homophobia". Part of Weinberg's definition of homophobia is "the dread of being in close quarters with homosexuals." (See his Society and the Healthy Homosexual.) In his now classic study, Homosexuality Reexamined, D.J. West wrote that "when placed in a situation that threatens to excite their own unwanted homosexual thoughts, they overreact with panic or anger."
New Atheism: Of all the New Atheists the worst, by far, are the self-appointed Science Nazis: Richard Dawkins, Sam Harris, PZ Meyers, Jerry Coyne and their ilk. One of their primary goals is to turn the world of scientific research into a "religion free zone", so that atheist scientists will have a safe refuge where they needn't dread being in close quarters with icky religious people and their spiritual cooties. At the very least they want to impose a "don't ask, don't tell" policy concerning religion among scientists. This aspect of New Atheism was especially noticeable in their frenzied response to Francis Collins' appointment as NIH Director.
7. Creepy obsessions
Homophobia: Rick Warren: "But the issue to me is, I’m not opposed to that as much as I’m opposed to the redefinition of a 5,000-year definition of marriage. I’m opposed to having a brother and sister be together and call that marriage. I’m opposed to an older guy marrying a child and calling that a marriage. I’m opposed to one guy having multiple wives and calling that marriage."
New Atheism: Richard Dawkins: "Imagine, with John Lennon, a world with no religion. Imagine no suicide bombers, no 9/11, no 7/7/, no Crusades, no witch-hunts, no Gunpowder Plot, no Indian partition, no Israeli/Palestinian wars, no Serb/Croat/Muslim massacres, no persecution of Jews as 'Christ-killers', no Northern Ireland 'troubles', no 'honour killings', no shiny suited bouffant-haired televangelists fleecing gullible people of their money."